Such as?
Only way the game would have been coherent was if the protagonist was subject 16 and it was their first version of the Animus.
They created the Helix system in the most recent AC games, which are basically Animus as video game consoles.
They've mastered the bleeding effect which the protagonist suffers a lot from.
They're not looking for an Apple anymore.
They had already found one before the first game started actually.
In the movie, them finding the apple sounds like a big deal when they already had one and destroyed it in the games.
The templars gave up on their "control humanity with the Apple" plan, instead they want to recreate an Isu by finding DNA from Sages (descendants of the Isu) throughout history.
And so on, many details don't fit.
The movie is a retelling of the games but no way it is part of the games' canon.